LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-739-g2644e7f6fa-modified)
  using 1 OpenMP thread(s) per MPI task
# Solvated 5-mer peptide, run for 8ps in NVT

units           real
atom_style      full

pair_style      lj/charmm/coul/long 8.0 10.0 10.0
bond_style      harmonic
angle_style     charmm
dihedral_style  charmm
improper_style  harmonic
kspace_style    pppm 0.0001

read_data       data.peptide
Reading data file ...
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2004 atoms
  reading velocities ...
  2004 velocities
  scanning bonds ...
  3 = max bonds/atom
  scanning angles ...
  6 = max angles/atom
  scanning dihedrals ...
  14 = max dihedrals/atom
  scanning impropers ...
  1 = max impropers/atom
  orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  1365 bonds
  reading angles ...
  786 angles
  reading dihedrals ...
  207 dihedrals
  reading impropers ...
  12 impropers
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     7 = max # of 1-3 neighbors
    14 = max # of 1-4 neighbors
    18 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.013 seconds

neighbor        2.0 bin
neigh_modify    delay 5

thermo          50
#dump            dump1 all atom 100 peptide.dump

timestep        8

run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3
Respa levels:
  1 = bond angle
  2 = dihedral improper pair
  3 = kspace

fix             1 all nvt temp 250.0 250.0 100.0 tchain 1
fix             cor all filter/corotate m 1.0
  19 = # of size 2 clusters
  0 = # of size 3 clusters
  3 = # of size 4 clusters
  0 = # of size 5 clusters
  646 = # of frozen angles
run             1000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- Mollified Impulse Method with Corotational Filter: doi:10.1016/j.jcp.2016.12.024

@Article{Fath2017,
 Title ={A Fast Mollified Impulse Method for Biomolecular Atomistic Simulations},
 Author = {L. Fath and M. Hochbruck and C. V. Singh},
 Journal = {Journal of Computational Physics},
 Year = {2017},
 Pages = {180--198},
 Volume = {333},

 Doi = {https://doi.org/10.1016/j.jcp.2016.12.024},
 ISSN = {0021-9991},
 Keywords = {Mollified impulse method},
 Url = {https://www.sciencedirect.com/science/article/pii/S0021999116306787}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.26872465
  grid = 15 15 15
  stencil order = 5
  estimated absolute RMS force accuracy = 0.022820853
  estimated relative force accuracy = 6.872432e-05
  using double precision FFTW3
  3d grid and FFT values/proc = 10648 3375
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 12
  ghost atom cutoff = 12
  binsize = 6, bins = 5 5 5
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/charmm/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 23.05 | 23.05 | 23.05 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   190.0857      -6442.7438      70.391457     -5237.4338      20361.984    
        50   239.47653     -7205.1003      1092.7665     -4682.5242     -23733.122    
       100   244.07229     -6785.0504      422.90862     -4904.893       16449.416    
       150   239.52635     -7251.3287      955.01358     -4866.2081     -13683.407    
       200   249.88988     -6874.4712      567.51841     -4814.9696      10008.486    
       250   242.44532     -7302.2945      902.65029     -4952.1093     -9379.0629    
       300   254.21219     -6994.4761      656.85648     -4819.8298      6662.4155    
       350   251.99651     -7214.6827      823.07017     -4887.0516     -5847.4094    
       400   244.06253     -7069.8698      699.40399     -4913.2752      2210.4098    
       450   251.30796     -7192.0473      822.96919     -4868.6282     -3503.7561    
       500   254.45168     -7110.7365      728.19119     -4863.3256      3846.7772    
       550   246.31169     -7273.8597      822.51469     -4980.7256     -3223.6704    
       600   248.54734     -7155.4287      733.9911      -4937.4702      1999.1375    
       650   246.15897     -7203.0144      799.85949     -4933.4474     -2344.6157    
       700   246.72182     -7252.9263      805.26935     -4974.5889      619.73298    
       750   256.14222     -7204.8077      809.95543     -4865.5391     -2613.0228    
       800   247.6005      -7267.6092      828.9905      -4960.3044     -340.24603    
       850   245.82973     -7268.6642      810.23505     -4990.6874     -1391.3847    
       900   255.51077     -7290.2059      809.08122     -4955.5817      197.37923    
       950   241.56497     -7277.1054      826.60919     -5008.2174     -1531.0793    
      1000   255.02322     -7248.7635      819.70368     -4906.4278     -731.80171    
Loop time of 59.8112 on 1 procs for 1000 steps with 2004 atoms

Performance: 11.556 ns/day, 2.077 hours/ns, 16.719 timesteps/s, 33.505 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 55.349     | 55.349     | 55.349     |   0.0 | 92.54
Bond    | 0.54636    | 0.54636    | 0.54636    |   0.0 |  0.91
Kspace  | 0.43248    | 0.43248    | 0.43248    |   0.0 |  0.72
Neigh   | 2.183      | 2.183      | 2.183      |   0.0 |  3.65
Comm    | 0.48557    | 0.48557    | 0.48557    |   0.0 |  0.81
Output  | 0.00047146 | 0.00047146 | 0.00047146 |   0.0 |  0.00
Modify  | 0.68423    | 0.68423    | 0.68423    |   0.0 |  1.14
Other   |            | 0.1304     |            |       |  0.22

Nlocal:           2004 ave        2004 max        2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          11223 ave       11223 max       11223 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:         708048 ave      708048 max      708048 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 708048
Ave neighs/atom = 353.31737
Ave special neighs/atom = 2.3403194
Neighbor list builds = 200
Dangerous builds = 200
unfix           cor
unfix           1



Total wall time: 0:00:59
